Pakistan has given foreigners working for Save the Children a week to leave the country after becoming convinced that the aid organisation was used as cover by US spies hunting Osama bin Laden.

The aid group had been under suspicion from authorities ever since a doctor accused of assisting the CIA in its search for the al-Qaida leader claimed that Save the Children had introduced him to US intelligence officers.

But now Pakistani officials claim they have "concrete proof" backing up the story of Shakil Afridi, the doctor from the tribal areas bordering Afghanistan who confessed to the ISI, the country's military spy agency, after being arrested last year.

Although Save the Children and the US government have always denied any relationship between the CIA and the aid organisation, Pakistani officials say they are fully justified in expelling the few foreign staff still working in the country.

According to a foreign diplomat the six foreigners will have to leave by next Wednesday.

A Pakistani intelligence official said evidence had been found showing "spies" at the NGO had "engaged" Afridi, who is currently serving a 33 year jail term. "Pakistan carried out a thorough investigation involving all our leading agencies," he said. "It was one of the longest investigations in our history. It is a very serious matter and the foreign staff were asked to leave only after concrete proof was uncovered."

Afridi is accused of setting up a bogus hepatitis B vaccination campaign in the Abbottabad area to try to pinpoint Bin Laden's exact location.

Pakistani officials say blood samples, which it had been hoped would be collected from people living in the house where the terrorist leader was thought to be hiding, were to be tested by the CIA for genetic matches to Bin Laden.

Although Afridi never succeeded in persuading the occupants of the crowded building to give blood, his collaboration with a foreign intelligence service is regarded as an act of treason by Pakistan's security establishment.

Foreigners working in the country, including diplomats and aid workers, have been under intense suspicion ever since.

Embassies and aid groups have complained of harassment, tight restrictions on the movement of their staff and acute difficulty obtaining visas.

The expulsions come despite lobbying by western diplomats on behalf of a respected organisation which has been working in impoverished areas of the country for decades, including during the devastating 2010 floods when it assisted more than 3 million people.

Save the Children said on Wednesday it had "never knowingly employed anyone who works for the CIA, or any other security service".

"Dr Afridi was never employed by Save the Children, nor was he ever paid for any kind of work. We have never run a vaccination programme in Abbottabad," it said in a statement.

"Save the Children is a global organisation and has a zero-tolerance policy for people involved in work that is not humanitarian and does not benefit children and their families. We reiterate our offer to the Pakistani authorities to examine our country office financial records and interview any of our staff concerned with our operation there."

Save the Children recently restructured itself, merging previously autonomous branches run from the US, the UK and Sweden. The new organisation has been in protracted negotiations with the government about its future, with Pakistan so far refusing to sign an agreement formalising Save the Children's operations in the country.

The organisation said that only six of its 2,000 staff in Pakistan are foreign nationals and that it would "continue our daily work helping millions of children across Pakistan".

The CIA imposes some restrictions on itself over what cover its agents can use in the field. It is not known whether limits are placed on the use of foreign NGOs.

Members of the foreign aid community fear the claim that a leading NGO became entangled – even unwittingly – in the activities of the CIA could endanger staff and affect operations around the world.

Critics say the widely publicised story has already affected efforts to encourage parents to vaccinate their children against polio, the devastating leg withering disease that Pakistan is struggling to eradicate.

Many Pakistanis were already deeply suspicious of outside doctors coming to their areas even before Afridi, who used to run anti-polio campaigns, became publicly associated with the CIA.

Calls and text messages to officials at the interior ministry went unanswered on Wednesday.